One night in 2008, Tomczeszyn hid with Dacyshyn in the garage of FBIAgentMonica Bannan's home before hurriedly stepping out in front of her, unaware that Agent Bannan had already noticed evidence that her home was being intruded upon. Tomczeszyn was struck four times by Agent Bannan using a gardening tool. He cried out in pain during the attack and even after it, when he stared at his bloodied hand in horrified agony.

Tomczeszyn's severed arm.

After Dacyshyn succeeded in kidnapping Agent Bannan and the men put her in the back of Dacyshyn's snowplow, Tomczeszyn's arm was amputated, wrapped in a sheet of black plastic and buried in a snow-covered field about ten miles from Agent Bannan's home. In the tissue of Tomczeszyn's severed arm, there were traces of a drug commonly given to patients being treated with radiation as well as traces of an animal tranquilizer called acepromazine. Despite the abductors' attempt to hide the evidence by burying it, the FBI uncovered Tomczeszyn's severed arm soon after Agent Bannan went missing. As another consequence of being attacked by Agent Bannan, Tomczeszyn's bald head was permanently marked with long, parallel grooves.

Shortly after Father Joe cried tears of blood while unsuccessfully struggling to psychically see where Agent Bannan had been taken, Tomczeszyn lay on a gurney, under a green surgical shroud, as he began to cry tears of blood, himself.

Moments after the FBI discovered that Tomczeszyn was actually a former altar boy of Father Joe and had known him for over twenty years, Special AgentDrummy notified FBI consultant Fox Mulder of the finding, referring to Tomczeszyn as "an old friend of Father Joe's."

Both Tomczeszyn and Father Joe were ill with lung cancer. After Dr. Dana Scully showed Father Joe an image of Tomczeszyn (while the terminally ill Father Joe was resting at Scully's workplace of Our Lady of Sorrows Hospital), Joe claimed he was fairly certain that he did not know the pictured man but Scully implied that he had, in fact, known the picture's subject ever since Tomczeszyn had been a boy. A horrified Father Joe then realized the pictured man's identity. Although initially skeptical of his connection to Tomczeszyn, Father Joe soon came to the conclusion that, in a work of God, his visions had been to save the abductees from Tomczeszyn.

By the time Father Joe realized this connection, Tomczeszyn's head had been grafted to the lower body of Agent Bannan but his breathing had become labored and he continued to lie on the gurney. As Dacyshyn argued in Russian with a doctor responsible for the transplants, Tomczeszyn was approached by the two men and his right shoulder was examined by Dacyshyn before both of Tomczeszyn's visitors walked away from him. He was then approached by two assistants of the Russian doctor.

Preparations were subsequently made for Tomczeszyn's head to be joined to the lower body of Cheryl Cunningham, another abductee whom Dacyshyn had captured and whom Tomczeszyn had been watching – while she had been kept inside a wooden box – when he had begun to cry tears of blood. As a drugged Cheryl Cunningham was prepared for the procedure, Tomczeszyn's stitches – joining his neck to Monica Bannan's torso – were removed by the Russian doctor as Dacyshyn whispered caring reassurances to Tomczeszyn that he didn't need the body he was currently joined to and that he would survive to have a strong, healthy body. The doctors then connected Tomczeszyn's head to Cheryl Cunningham's blood supply and removed his head from Agent Bannan's lower body, which Dacyshyn chopped up and discarded.

Tomczeszyn's operation was interrupted by the arrival of the FBI – first, Mulder, then Scully and Assistant DirectorWalter Skinner. Scully removed Tomczeszyn's head from the blood supply. Following Tomczeszyn's death, Mulder implied that he believed the psychic connection between Tomczeszyn and Father Joe (who was now also dead) was evidenced by the fact that they had both had lung cancer. Mulder additionally suspected that Scully had cut off the blood supply to Tomczeszyn's head at exactly the same time when Father Joe had died and that this finding would be more proof to the FBI that the psychic connection had existed. (The X-Files: I Want to Believe)

The character is referred to in the film's end credits as "1st Abductor (Franz Tomczeszyn)". The character has the same last name as Costume Designer Lisa Tomczeszyn.

The fact that the Russian doctor is referred to, in a newspaper clipping seen in the film, as a "modern day Frankenstein doctor" would seem to imply that – in the same analogy – Tomczeszyn would be the Frankenstein's monster. In fact, Chris Carter does refer to Tomczeszyn as "the Frankenstein monster", in the film's audio commentary.

The illusion of Tomczeszyn's head attached to Agent Bannan's lower body was created with a sculpting of Agent Bannan's lower body and a gurney that had a hole through it; the prosthetic body would lie on the gurney, above the hole, through which the actor was then able to maneuver his head, and a velcro attachment at the neck of the prosthetic body would wrap around the actor's neck, fastening the actor to the body sculpting. The prosthetic body was not required to be moved from the gurney so it was specifically built for virtually no articulation, except to create the illusion of Tomczeszyn using the body to breath. To create the breathing effect, special makeup effects designer Bill Terezakis incorporated a device (into the lower body) that was essentially a tube and a member of the film crew blew through the tube, while under the gurney. Blowing quicker through the tube would give the impression that the chest was hyperventilating.

Another model was built to resemble Tomczeszyn's severed head; it was used for close-up shots of the head and could be made to blink.

Preliminary concept art of Tomczeszyn's severed arm was created, and an extraordinarily detailed and articulate model of the arm was ultimately built.